Preprocessing QC statistics

Noam, July 2023

In [1]:
%load_ext autoreload
%autoreload 2
In [2]:
import os
MOMAPS_HOME = '/home/labs/hornsteinlab/Collaboration/MOmaps'
LOGS_PATH = os.path.join(MOMAPS_HOME, 'src', 'preprocessing', 'logs')
os.chdir(MOMAPS_HOME)
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
sns.set(style="whitegrid", font_scale=1.5)
sns.color_palette("husl", 8)
plt.rcParams["image.cmap"] = "Set1"
from tqdm.notebook import tqdm
from src.common.lib.preprocessing_utils import rescale_intensity
from src.common.lib.images_qc import *
sys.path.insert(1, "/home/labs/hornsteinlab/Collaboration/MOmaps_Sagy/MOmaps/src/common/lib")
import contextlib
import io
from calc_dataset_variance import calc_variance_neurons_batch
import matplotlib
import warnings
warnings.filterwarnings('ignore', category=pd.core.common.SettingWithCopyWarning)
In [3]:
df = log_files_qc(LOGS_PATH)
Total of 12 files were read.
Before dup handeling  (137406, 20)
After duplication removal #1: (137220, 21)
After duplication removal #2: (135908, 21)

validate folder structure and files existence

In [4]:
# choose batches
batches = [f'batch{i}' for i in range (3,10)] + ['batch7_16bit','batch8_16bit','batch9_16bit']

Raw Files

In [5]:
root_directory_raw = os.path.join(MOMAPS_HOME, 'input', 'images', 'raw', 'SpinningDisk')

batches_raw = [batch.replace("_16bit","") for batch in batches]
raws = run_validate_folder_structure(root_directory_raw, proc=False, batches=batches_raw, per=False)
batch3
Folder structure is invalid. Missing paths:
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/FUSHomozygous/panelA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/FUSHomozygous/panelB
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/FUSHomozygous/panelC
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/TDP43/panelA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/TDP43/panelB
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/TDP43/panelC
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/TBK1/panelA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/TBK1/panelB
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/TBK1/panelC
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/WT/panelA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/WT/panelB
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/WT/panelC
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/SCNA/panelA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/SCNA/panelB
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/SCNA/panelC
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/FUSRevertant/panelA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/FUSRevertant/panelB
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/FUSRevertant/panelC
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/OPTN/panelA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/OPTN/panelB
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/OPTN/panelC
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/FUSHeterozygous/panelA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/FUSHeterozygous/panelB
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch3/FUSHeterozygous/panelC
Some files are bad:
CellProfiler_output
CellProfiler_output
========
batch4
Folder structure is valid.
All files exists.
========
batch5
Folder structure is valid.
All files exists.
========
batch6
Folder structure is valid.
All files exists.
========
batch7
Folder structure is valid.
All files exists.
========
batch8
Folder structure is valid.
All files exists.
========
batch9
Folder structure is valid.
All files exists.
========
batch7
Folder structure is valid.
All files exists.
========
batch8
Folder structure is valid.
All files exists.
========
batch9
Folder structure is valid.
All files exists.
========
====================

Processed

In [6]:
root_directory_proc = os.path.join(MOMAPS_HOME, 'input', 'images', 'processed', 'spd2',
                              'SpinningDisk')
procs = run_validate_folder_structure(root_directory_proc, proc=True, batches=batches)
batch3
Folder structure is invalid. Missing paths:
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHomozygous/Untreated/G3BP1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHomozygous/Untreated/NONO
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHomozygous/Untreated/SQSTM1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHomozygous/Untreated/KIF5A
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHomozygous/Untreated/TDP43
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHomozygous/Untreated/FMRP
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHomozygous/Untreated/PURA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHomozygous/Untreated/CD41
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHomozygous/Untreated/Phalloidin
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TDP43/Untreated/G3BP1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TDP43/Untreated/NONO
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TDP43/Untreated/SQSTM1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TDP43/Untreated/KIF5A
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TDP43/Untreated/TDP43
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TDP43/Untreated/FMRP
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TDP43/Untreated/PURA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TDP43/Untreated/CD41
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TDP43/Untreated/Phalloidin
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TBK1/Untreated/G3BP1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TBK1/Untreated/NONO
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TBK1/Untreated/SQSTM1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TBK1/Untreated/KIF5A
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TBK1/Untreated/TDP43
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TBK1/Untreated/FMRP
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TBK1/Untreated/PURA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TBK1/Untreated/CD41
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/TBK1/Untreated/Phalloidin
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/stress/G3BP1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/stress/NONO
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/stress/SQSTM1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/stress/KIF5A
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/stress/TDP43
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/stress/FMRP
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/stress/PURA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/stress/CD41
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/stress/Phalloidin
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/Untreated/G3BP1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/Untreated/NONO
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/Untreated/SQSTM1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/Untreated/KIF5A
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/Untreated/TDP43
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/Untreated/FMRP
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/Untreated/PURA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/Untreated/CD41
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/WT/Untreated/Phalloidin
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/SCNA/Untreated/G3BP1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/SCNA/Untreated/NONO
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/SCNA/Untreated/SQSTM1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/SCNA/Untreated/KIF5A
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/SCNA/Untreated/TDP43
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/SCNA/Untreated/FMRP
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/SCNA/Untreated/PURA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/SCNA/Untreated/CD41
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/SCNA/Untreated/Phalloidin
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSRevertant/Untreated/G3BP1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSRevertant/Untreated/NONO
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSRevertant/Untreated/SQSTM1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSRevertant/Untreated/KIF5A
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSRevertant/Untreated/TDP43
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSRevertant/Untreated/FMRP
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSRevertant/Untreated/PURA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSRevertant/Untreated/CD41
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSRevertant/Untreated/Phalloidin
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/OPTN/Untreated/G3BP1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/OPTN/Untreated/NONO
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/OPTN/Untreated/SQSTM1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/OPTN/Untreated/KIF5A
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/OPTN/Untreated/TDP43
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/OPTN/Untreated/FMRP
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/OPTN/Untreated/PURA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/OPTN/Untreated/CD41
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/OPTN/Untreated/Phalloidin
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHeterozygous/Untreated/G3BP1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHeterozygous/Untreated/NONO
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHeterozygous/Untreated/SQSTM1
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHeterozygous/Untreated/KIF5A
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHeterozygous/Untreated/TDP43
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHeterozygous/Untreated/FMRP
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHeterozygous/Untreated/PURA
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHeterozygous/Untreated/CD41
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch3/FUSHeterozygous/Untreated/Phalloidin
All files exists.
========
batch4
Folder structure is valid.
All files exists.
========
batch5
Folder structure is valid.
All files exists.
========
batch6
Folder structure is valid.
All files exists.
========
batch7
Folder structure is valid.
All files exists.
========
batch8
Folder structure is valid.
All files exists.
========
batch9
Folder structure is valid.
Some files are bad:
rep1_R11_w3confCy5_s1497_panelE_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w3confCy5_s1417_panelE_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w2confmCherry_s1409_panelB_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w2confmCherry_s1421_panelB_FUSRevertant_processed.npy small size (0.128 kB)
rep2_R11_w2confmCherry_s1552_panelF_FUSRevertant_processed.npy small size (0.128 kB)
rep2_R11_w2confmCherry_s1574_panelF_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w2confmCherry_s1421_panelH_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w2confmCherry_s1409_panelH_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w2confmCherry_s1409_panelI_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w2confmCherry_s1421_panelI_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w2confmCherry_s1421_panelJ_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w2confmCherry_s1409_panelJ_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w4confGFP_s1416_panelK_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w4confGFP_s1429_panelK_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w1confDAPI_s1417_panelA_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w1confDAPI_s1465_panelA_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w1confDAPI_s550_panelG_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w1confDAPI_s1417_panelD_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w1confDAPI_s1417_panelC_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w1confDAPI_s586_panelG_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w1confDAPI_s1465_panelD_FUSRevertant_processed.npy small size (0.128 kB)
rep1_R11_w1confDAPI_s1465_panelC_FUSRevertant_processed.npy small size (0.128 kB)
========
batch7_16bit
Folder structure is valid.
All files exists.
========
batch8_16bit
Folder structure is valid.
All files exists.
========
batch9_16bit
Folder structure is valid.
All files exists.
========
====================

Difference between Raw and Processed

In [7]:
display_diff(batches, raws, procs)
batch3
========
batch4
========
batch5
========
batch6
========
batch7
========
batch8
========
batch9
========
batch7_16bit
========
batch8_16bit
========
batch9_16bit
========
In [10]:
for batch in list(range(3,9)) + ['7_16bit','8_16bit','9_16bit']: #problem with batch9: files that are 1 bytes!!!
    with contextlib.redirect_stdout(io.StringIO()):
        var = calc_variance_neurons_batch(batch_num=batch)
    print(f'batch{batch} var: ',var)
    
batch3 var:  0.008985334561550524
batch4 var:  0.008887061453338514
batch5 var:  0.008859492150719803
batch6 var:  0.012074356060396271
batch7 var:  0.011567470159263302
batch8 var:  0.012385897273422274
batch7_16bit var:  0.009461290806041153
batch8_16bit var:  0.009776277165818721
batch9_16bit var:  0.009599798918941808

Number of sites in each batch and cell line

In [9]:
plot_sites_count(df, split_to_reps=True)

Number of Cells in Site for each batch and cell line

In [11]:
df_no_empty_sites = df[df.n_valid_tiles !=0]
plot_cell_count(df_no_empty_sites, whole_cells=True, per=False)

plot_cell_count(df_no_empty_sites, whole_cells=False, per=False)
# can add norm=True to norm by max

number of valid tiles per image (site)

In [17]:
plot_n_valid_tiles_count(df, per=False)

Heatmap QC per batch, panel and cell line(tiles that passed QC condition)

In [12]:
plot_hm(df, per=False)
In [13]:
# # save notebook as HTML ( the HTML will be saved in the same folder the original script is)
# from IPython.display import display, Javascript
# display(Javascript('IPython.notebook.save_checkpoint();'))
# os.system('jupyter nbconvert --to html src/preprocessing/notebooks/cell_count_stats_analysis_Noam.ipynb')

Assessing Staining Reproducibility and Outliers

In [14]:
for batch in batches:
    if batch=='batch9' or batch=='batch3' or '16_bit' in batch:
        continue
    print(batch)
    batch_num = batch.replace('batch',"")
    run_calc_hist_new(batch_num=batch_num,sample_size_per_markers=10)
    print("="*30)
batch4


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch4, _sample_size_per_markers:10, _num_markers:72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 1440 sampled_markers: 144
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch4, _sample_size_per_markers:20, _num_markers:26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 1040 sampled_markers: 52
sampled_images: 510 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26


Total of 6480 images were sampled for hist calculation.


Total of 4670 images were sampled for hist calculation.
/home/labs/hornsteinlab/Collaboration/MOmaps/src/common/lib/images_qc.py:844: UserWarning: This figure includes Axes that are not compatible with tight_layout, so results might be incorrect.
  plt.tight_layout()
/home/labs/hornsteinlab/nancyy/.local/lib/python3.7/site-packages/IPython/core/pylabtools.py:151: UserWarning: This figure includes Axes that are not compatible with tight_layout, so results might be incorrect.
  fig.canvas.print_figure(bytes_io, **kw)
==============================
batch5


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch5, _sample_size_per_markers:10, _num_markers:72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 1440 sampled_markers: 144
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch5, _sample_size_per_markers:20, _num_markers:26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 1040 sampled_markers: 52
sampled_images: 514 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26


Total of 6480 images were sampled for hist calculation.


Total of 4674 images were sampled for hist calculation.
==============================
batch6


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch6, _sample_size_per_markers:10, _num_markers:72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 1440 sampled_markers: 144
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch6, _sample_size_per_markers:20, _num_markers:26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 1040 sampled_markers: 52
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26


Total of 6480 images were sampled for hist calculation.


Total of 4680 images were sampled for hist calculation.
==============================
batch7


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch7, _sample_size_per_markers:10, _num_markers:72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 1440 sampled_markers: 144
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch7, _sample_size_per_markers:20, _num_markers:26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 1040 sampled_markers: 52
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26


Total of 6480 images were sampled for hist calculation.


Total of 4680 images were sampled for hist calculation.
==============================
batch8


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch8, _sample_size_per_markers:10, _num_markers:72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 1440 sampled_markers: 144
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch8, _sample_size_per_markers:20, _num_markers:26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 1040 sampled_markers: 52
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26


Total of 6480 images were sampled for hist calculation.


Total of 4680 images were sampled for hist calculation.
==============================
batch7_16bit


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch7, _sample_size_per_markers:10, _num_markers:72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 1440 sampled_markers: 144
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch7_16bit, _sample_size_per_markers:20, _num_markers:26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 1040 sampled_markers: 52
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26


Total of 6480 images were sampled for hist calculation.


Total of 4680 images were sampled for hist calculation.
==============================
batch8_16bit


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch8, _sample_size_per_markers:10, _num_markers:72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 1440 sampled_markers: 144
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch8_16bit, _sample_size_per_markers:20, _num_markers:26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 1040 sampled_markers: 52
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26


Total of 6480 images were sampled for hist calculation.


Total of 4680 images were sampled for hist calculation.
==============================
batch9_16bit


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/raw/SpinningDisk/batch9, _sample_size_per_markers:10, _num_markers:72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 1440 sampled_markers: 144
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72
sampled_images: 720 sampled_markers: 72


[sample_images_all_markers_all_lines]: input_dir_batch:/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/spd2/SpinningDisk/batch9_16bit, _sample_size_per_markers:20, _num_markers:26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 1040 sampled_markers: 52
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26
sampled_images: 520 sampled_markers: 26


Total of 6480 images were sampled for hist calculation.


Total of 4680 images were sampled for hist calculation.
==============================
In [15]:
print(os.system('pwd'))
print("Done!")
/home/labs/hornsteinlab/Collaboration/MOmaps
0
Done!